Problem viewing files in Lightroom 2.6

Am using OS Windows 7, 64 bit. Have inages stored on an external USB hard Drive (320 GB Toshiba) and use an 8 GB thumb drive for administrative files. With both devices plugged in I open Lightroom and see the following:
Catalog>All Photographs: 21,526
Folders>Home (L:) [thumb]: 19,433 photos
          >Aggie (O:) [Toshiba]:  2,093 photos
Indicator light to left of "Home" is orange.
Indicator light to left of "Aggie" is Black or Green.
Problem One:  The desktop seems to find "Aggie" and then lose her - cycling "On" an "Off" so to speak and for no apparent reason. The drive is not being moved, cables jiggled or anything discernable. This cycling might happen every minute or so. This does not appear to be a function of the drive because I can work in the directory in Explore and drag and drop files, e.g., without any difficulty. So, the question here is -- is this a problem within Lightroom or even in the OS.
Problem Two:  The 19,433 photos that Lightroom indicates as being in the "Home" folder simply are not there! They are, in fact, on "Aggie". I prove this by doing a *.DNG search in the "Home" directory which comes up empty. The 2,093 photos which do show up in "Aggie" where they belong are recent imports -- possibly since upgrading to Windows 7.
Questions:
    1.   Does anyone have a clue why the hard drive might be dropping out and/or cycling?
     2.  How is it possible that files which are clearly on one drive will show up in Lightroom as being on another drive?
     3.  Why is it that when the indicator light on "Aggie" is Green the folders on that drive still have a "?" beside them?    

Maybe I am misunderstanding your terminology, but are you saying you have 19,433 photos on a 8GB drive?
If any folder is showing a ?, then right click on it and locate the folder on the drive.

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